Locus 2710

Sequence ID dm3.chr2L
Location 21,423,135 – 21,423,190
Length 55
Max. P 0.999859
window3716 window3717

overview

Window 6

Location 21,423,135 – 21,423,190
Length 55
Sequences 11
Columns 66
Reading direction forward
Mean pairwise identity 58.05
Shannon entropy 0.88502
G+C content 0.46956
Mean single sequence MFE -18.47
Consensus MFE -11.74
Energy contribution -13.01
Covariance contribution 1.27
Combinations/Pair 1.50
Mean z-score -2.01
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.60
SVM RNA-class probability 0.999859
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 21423135 55 + 23011544
AUUGUGGCCUUGAAAAGGGCCGUUUUGGAUUAUUGUCCGCA---UUCGCAGGAGAAAA--------
.((((((((((....)))))).....((((....))))...---...)))).......-------- ( -17.40, z-score =  -1.81, R)
>droSim1.chrU 65411 55 - 15797150
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUGUUGUCCGCA---UUCGCAGGAGCCAA--------
.....((((((....))))))(((((((((....))))((.---...)).)))))...-------- ( -21.60, z-score =  -2.34, R)
>droSec1.super_91 64049 53 + 125313
AUUGUGGCC-UGAAAAGGGCCGUUUUGAAUUGUUGUCCGCA---UUCGCAGGAGCCA---------
.....((((-(.....)))))..............(((((.---...)).)))....--------- ( -13.10, z-score =   0.18, R)
>droYak2.chr2R_random 60460 58 - 67238
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUAAUGUCCGCAGCAUUCGUAGGAACAAA--------
.((((((((((....))))))(((.(((((....))))).)))..........)))).-------- ( -23.20, z-score =  -3.62, R)
>droEre2.scaffold_4845 19535491 55 - 22589142
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUUUUGUCCGCA---CUCGCAGGAGGAAA--------
..(((((((((....)))))).....((((....)))))))---(((....)))....-------- ( -21.40, z-score =  -2.38, R)
>droAna3.scaffold_12943 4809564 54 - 5039921
GUUGUGGCCCUGAAAAGGGCCUUUUUGGAUCAUUCUGCCCA----GCAAGCGAGCAAU--------
((((.((((((....)))))).....(((....)))...))----))...........-------- ( -17.50, z-score =  -0.99, R)
>droWil1.scaffold_181036 1021 60 + 110856
AUUGUGGCCCUGAAAAGGGCUUUUUUUUUAAAAGGAAGCGUGUGUUUAAGCUAGGGACAU------
.((.(((((((....)))((((((((.....))))))))..........)))).))....------ ( -14.80, z-score =  -0.85, R)
>droVir3.scaffold_13047 1585291 66 + 19223366
UUUGUGGCCCUGAAAAGGGCCUUUUGCUUUUGUUUGCUUCCCGUACAAUGCACAUCUAGCUGAAUU
.....((((((....))))))(((.(((...((.(((............))).))..))).))).. ( -18.20, z-score =  -1.84, R)
>droMoj3.scaffold_6540 26857080 64 - 34148556
UUUGUGGCCCUGAAAAGGGCCUUUUGCUUCUUCUU--UUGGAAUUCUGCAUACACCGAGGUAAGAU
.....((((((....))))))(((((((((.....--.((.(....).))......))))))))). ( -20.80, z-score =  -2.43, R)
>droGri2.scaffold_14978 482894 52 + 1124632
UUUGUGGCCCUGAAAAGGGCCUUUUGCUGCUAAC----UGGUUUUCUGCCUGCAAU----------
.....((((((....))))))......(((....----.(((.....))).)))..---------- ( -18.20, z-score =  -2.45, R)
>anoGam1.chrU 44504713 52 + 59568033
UUUGUGGUCCUGAAAAGGACCGAUUUGAGAGAGGUUCAUGA------AAAGAAGCCAA--------
....(((((((....)))))))..........((((..(..------..)..))))..-------- ( -17.00, z-score =  -3.59, R)
>consensus
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUAUUGUCCGCA___UUCGCAGGAGCCAA________
.....((((((....))))))............................................. (-11.74 = -13.01 +   1.27)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 21,423,135 – 21,423,190
Length 55
Sequences 11
Columns 66
Reading direction reverse
Mean pairwise identity 58.05
Shannon entropy 0.88502
G+C content 0.46956
Mean single sequence MFE -14.25
Consensus MFE -10.06
Energy contribution -10.16
Covariance contribution 0.11
Combinations/Pair 1.17
Mean z-score -1.50
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.97
SVM RNA-class probability 0.999519
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 21423135 55 - 23011544
--------UUUUCUCCUGCGAA---UGCGGACAAUAAUCCAAAACGGCCCUUUUCAAGGCCACAAU
--------.......((((...---.))))...............((((........))))..... ( -11.20, z-score =  -1.25, R)
>droSim1.chrU 65411 55 + 15797150
--------UUGGCUCCUGCGAA---UGCGGACAACAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
--------(((..(((.((...---.)))))...)))........((((((....))))))..... ( -16.30, z-score =  -1.62, R)
>droSec1.super_91 64049 53 - 125313
---------UGGCUCCUGCGAA---UGCGGACAACAAUUCAAAACGGCCCUUUUCA-GGCCACAAU
---------......((((...---.))))...............((((.......-))))..... ( -10.90, z-score =  -0.27, R)
>droYak2.chr2R_random 60460 58 + 67238
--------UUUGUUCCUACGAAUGCUGCGGACAUUAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
--------(((((....)))))......(((......))).....((((((....))))))..... ( -15.40, z-score =  -2.01, R)
>droEre2.scaffold_4845 19535491 55 + 22589142
--------UUUCCUCCUGCGAG---UGCGGACAAAAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
--------.......((((...---.))))...............((((((....))))))..... ( -15.70, z-score =  -1.81, R)
>droAna3.scaffold_12943 4809564 54 + 5039921
--------AUUGCUCGCUUGC----UGGGCAGAAUGAUCCAAAAAGGCCCUUUUCAGGGCCACAAC
--------.(((((((.....----))))))).............((((((....))))))..... ( -18.10, z-score =  -1.59, R)
>droWil1.scaffold_181036 1021 60 - 110856
------AUGUCCCUAGCUUAAACACACGCUUCCUUUUAAAAAAAAAGCCCUUUUCAGGGCCACAAU
------.(((....(((..........)))................(((((....))))).))).. (  -8.00, z-score =  -0.71, R)
>droVir3.scaffold_13047 1585291 66 - 19223366
AAUUCAGCUAGAUGUGCAUUGUACGGGAAGCAAACAAAAGCAAAAGGCCCUUUUCAGGGCCACAAA
......(((...(((((...)))))...)))..............((((((....))))))..... ( -18.30, z-score =  -1.74, R)
>droMoj3.scaffold_6540 26857080 64 + 34148556
AUCUUACCUCGGUGUAUGCAGAAUUCCAA--AAGAAGAAGCAAAAGGCCCUUUUCAGGGCCACAAA
....(((....)))..(((....(((...--..)))...)))...((((((....))))))..... ( -15.10, z-score =  -1.13, R)
>droGri2.scaffold_14978 482894 52 - 1124632
----------AUUGCAGGCAGAAAACCA----GUUAGCAGCAAAAGGCCCUUUUCAGGGCCACAAA
----------.((((..((.........----))..)))).....((((((....))))))..... ( -15.60, z-score =  -1.78, R)
>anoGam1.chrU 44504713 52 - 59568033
--------UUGGCUUCUUU------UCAUGAACCUCUCUCAAAUCGGUCCUUUUCAGGACCACAAA
--------..((.(((...------....)))))...........((((((....))))))..... ( -12.10, z-score =  -2.56, R)
>consensus
________UUGGCUCCUGCGAA___UGCGGACAAUAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
.............................................((((((....))))))..... (-10.06 = -10.16 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:56:20 2011